From Genome Analysis Wiki
→Phasing/Imputation with External Reference
When you phase/impute with external reference panel, you will only need to break the reference files into parts containing subsets of markers because SNPs in your own data (pedigree files) but not in reference files will be automatically ignored by MaCH and minimac. <br>
You can split the reference data using [http://
www.sph.umich.edu/ csg/yli/splitRef/ splitRef].
== Post Phasing/Imputation Ligation ==